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Tao Q, Wu Q, Xue Y, Chen C, Zhou Y, Shao R, Zhang H, Liu H, Zeng X, Zhou L, Liu Q, Jin H. Prognostic impact of IL7R mutations on acute myeloid leukemia. Ther Adv Hematol 2024; 15:20406207241279533. [PMID: 39346679 PMCID: PMC11439168 DOI: 10.1177/20406207241279533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/24/2024] [Indexed: 10/01/2024] Open
Abstract
Background Interleukin-7 receptor (IL7R) mutation has been demonstrated to be an adverse prognostic factor in acute lymphoblastic leukemia (ALL) patients. However, the effects of the IL7R mutation on acute myeloid leukemia (AML) have rarely been reported. Here, we investigated IL7R mutations and their effects on AML patients. Methods A total of 346 newly diagnosed AML patients from January 2017 to July 2020 at Nanfang Hospital were analyzed in this study. A genomic panel of 167 gene targets was detected by next-generation sequencing. Results Among 346 patients, 33 (9.5%) AML patients carried IL7R mutations. With a median follow-up of 50.7 months (95% confidence interval (CI) 17.3-62.2), the 5-year overall survival (OS) rates were 51.5% (95% CI 37.0%-71.0%) and 72.2% (95% CI 67.4%-77.3%; p = 0.008), the 5-year event-free survival (EFS) rates were 36.1% (95% CI 23.2%-57.1%) and 58.1% (95% CI 52.9%-63.8%; p = 0.005), the 5-year non-relapse mortality (NRM) were 21.4% (95% CI 8.5%-38.2%) and 6.2% (95% CI 3.7%-9.5%; p = 0.004) in the IL7R mutant (IL7R MUT ) group and non-IL7R mutant (IL7R WT ) group, respectively. There is no significant difference in the disease-free survival (75.1% vs 73.5%, p = 0.885) and cumulative incidence of relapse (25.7% vs 25.2%, p = 0.933) between IL7R MUT and IL7R WT group. Furthermore, patients who underwent hematopoietic stem cell transplantation (HSCT) still had more adverse outcomes in the IL7R MUT group than in the IL7R WT group (5-year OS: 61.9% vs 85.3%, p = 0.003). In the TET2 (p = 0.013) and DNA methyltransferase 3A (DNMT3A; p = 0.046) mutation subgroups, the presence of IL7R mutations was associated with worse OS than in AML patients without IL7R mutations. Conclusion Our study demonstrated that the IL7R mutation is associated with an inferior prognosis for AML patients. Patients with IL7R mutations have higher NRM, shorter OS, and EFS than patients without IL7R mutations, even patients who have undergone HSCT. Future larger and multicentric prospective studies will be explored.
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Affiliation(s)
- Qiqi Tao
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Hematology, The Sixth Affiliated Hospital, school of Medicine, South China University of Technology, Foshan, China
| | - Qiaoyuan Wu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Yutong Xue
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Changkun Chen
- Department of Hematology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, Jiangxi, China
- Department of Hematology, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
| | - Ya Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Ruoyang Shao
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Haiyan Zhang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | | | - Xiangzong Zeng
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Hematology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
| | - Lingling Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
| | - Hua Jin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Hematology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, Jiangxi, China
- Clinical Medical Research Center of Hematology Diseases of Guangdong Province, Guangzhou, China
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Woo AYH, Jia L. ALDH2 mutations and defense against genotoxic aldehydes in cancer and inherited bone marrow failure syndromes. Mutat Res 2024; 829:111870. [PMID: 38944932 DOI: 10.1016/j.mrfmmm.2024.111870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024]
Abstract
Reactive aldehydes, for instance, formaldehyde and acetaldehyde, are important endogenous or environmental mutagens by virtue of their abilities to produce a DNA lesion called interstrand crosslink (ICL). Aldehyde-metabolizing enzymes such as aldehyde dehydrogenases (ALDHs) and the Fanconi anemia (FA) pathway constitute the main defense lines against aldehyde-induced genotoxicity. Biallelic mutations of genes in any one of the FA complementation groups can impair the ICL repair mechanism and cause FA, a heterogeneous disorder manifested by bone marrow failure (BMF), congenital abnormality and a strong predisposition to cancer. The defective ALDH2 polymorphism rs671 (ALDH2*2) is a known risk and prognostic factor for alcohol drinking-associated cancers. Recent studies suggest that it also promotes BMF and cancer development in FA, and its combination with alcohol dehydrogenase 5 (ADH5) mutations causes aldehyde degradation deficiency syndrome (ADDS), also known by its symptoms as aplastic anemia, mental retardation, and dwarfism syndrome. ALDH2*2 and another pathogenic variant in the alcohol-metabolizing pathway, ADH1B1*1, is prevalent among East Asians. Also, other ALDH2 genotypes with disease-modifying potentials have lately been identified in different populations. Therefore, it would be appropriate to summarize current knowledge of genotoxic aldehydes and defense mechanisms against them to shed new light on the pathogenic effects of ALDH2 variants together with other genetic and environmental modifiers on cancer and inherited BMF syndromes. Lastly, we also presented potential treatment strategies for FA, ADDS and cancer based on the manipulation of aldehyde-induced genotoxicity.
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Affiliation(s)
- Anthony Yiu-Ho Woo
- School of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China.
| | - Lina Jia
- School of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
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Dubey AK, Kaur I, Madaan R, Raheja S, Bala R, Garg M, Kumar S, Lather V, Mittal V, Pandita D, Gundamaraju R, Singla RK, Sharma R. Unlocking the potential of oncology biomarkers: advancements in clinical theranostics. Drug Metab Pers Ther 2024; 39:5-20. [PMID: 38469723 DOI: 10.1515/dmpt-2023-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/11/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION Cancer biomarkers have revolutionized the field of oncology by providing valuable insights into tumor changes and aiding in screening, diagnosis, prognosis, treatment prediction, and risk assessment. The emergence of "omic" technologies has enabled biomarkers to become reliable and accurate predictors of outcomes during cancer treatment. CONTENT In this review, we highlight the clinical utility of biomarkers in cancer identification and motivate researchers to establish a personalized/precision approach in oncology. By extending a multidisciplinary technology-based approach, biomarkers offer an alternative to traditional techniques, fulfilling the goal of cancer therapeutics to find a needle in a haystack. SUMMARY AND OUTLOOK We target different forms of cancer to establish a dynamic role of biomarkers in understanding the spectrum of malignancies and their biochemical and molecular characterization, emphasizing their prospective contribution to cancer screening. Biomarkers offer a promising avenue for the early detection of human cancers and the exploration of novel technologies to predict disease severity, facilitating maximum survival and minimum mortality rates. This review provides a comprehensive overview of the potential of biomarkers in oncology and highlights their prospects in advancing cancer diagnosis and treatment.
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Affiliation(s)
- Ankit Kumar Dubey
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Reecha Madaan
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Shikha Raheja
- Jan Nayak Ch. Devi Lal Memorial College of Pharmacy, Sirsa, Haryana, India
| | - Rajni Bala
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research, 77282 Amity University, Sector-125 , Noida, India
| | - Suresh Kumar
- Department of Pharmaceutical Sciences and Drug Research, 429174 Punjabi University Patiala , Patiala, India
| | - Viney Lather
- Amity Institute of Pharmacy, 77282 Amity University , Noida, India
| | - Vineet Mittal
- Department of Pharmaceutical Sciences, 29062 Maharshi Dayanand University , Rohtak, Haryana, India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, PushpVihar, 633274 Govt. of NCT of Delhi , New Delhi, India
- Centre for Advanced Formulation and Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, PushpVihar, Govt. of NCT of Delhi, New Delhi, India
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, 8785 University of Tasmania , Launceston, Tasmania, Australia
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- School of Pharmaceutical Sciences, 34753 Lovely Professional University , Phagwara, Punjab, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, 80095 Banaras Hindu University , Varanasi, Uttar Pradesh, India
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Kechin A, Boyarskikh U, Borobova V, Khrapov E, Subbotin S, Filipenko M. BRACNAC: A BRCA1 and BRCA2 Copy Number Alteration Caller from Next-Generation Sequencing Data. Int J Mol Sci 2023; 24:16630. [PMID: 38068953 PMCID: PMC10706169 DOI: 10.3390/ijms242316630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Detecting copy number variations (CNVs) and alterations (CNAs) in the BRCA1 and BRCA2 genes is essential for testing patients for targeted therapy applicability. However, the available bioinformatics tools were initially designed for identifying CNVs/CNAs in whole-genome or -exome (WES) NGS data or targeted NGS data without adaptation to the BRCA1/2 genes. Most of these tools were tested on sample cohorts of limited size, with their use restricted to specific library preparation kits or sequencing platforms. We developed BRACNAC, a new tool for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes in NGS data of different origin. The underlying mechanism of this tool involves various coverage normalization steps complemented by CNV probability evaluation. We estimated the sensitivity and specificity of our tool to be 100% and 94%, respectively, with an area under the curve (AUC) of 94%. The estimation was performed using the NGS data obtained from 213 ovarian and prostate cancer samples tested with in-house and commercially available library preparation kits and additionally using multiplex ligation-dependent probe amplification (MLPA) (12 CNV-positive samples). Using freely available WES and targeted NGS data from other research groups, we demonstrated that BRACNAC could also be used for these two types of data, with an AUC of up to 99.9%. In addition, we determined the limitations of the tool in terms of the minimum number of samples per NGS run (≥20 samples) and the minimum expected percentage of CNV-negative samples (≥80%). We expect that our findings will improve the efficacy of BRCA1/2 diagnostics. BRACNAC is freely available at the GitHub server.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Viktoriya Borobova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Sergey Subbotin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
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Goyal PA, Bankar NJ, Mishra VH, Borkar SK, Makade JG. Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques. Cureus 2023; 15:e47106. [PMID: 38022057 PMCID: PMC10646819 DOI: 10.7759/cureus.47106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Molecular and genomic approaches have revolutionized medical microbiology by offering faster and more accurate diagnostic techniques for infectious diseases. Traditional methods, which include culturing microbes and biochemical testing, are time-consuming and may not detect antibiotic-resistant strains. In contrast, molecular and genomic methods, including polymerase chain reaction (PCR)-based techniques and whole-genome sequencing, provide rapid and precise detection of pathogens, early-stage diseases, and antibiotic-resistant strains. These approaches have advantages such as high sensitivity and specificity, the potential for targeted therapies, and personalized medicine. However, implementing molecular and genomic techniques faces challenges related to cost, equipment, expertise, and data analysis. Ethical and legal considerations regarding patient privacy and genetic data usage also arise. Nonetheless, the future of medical microbiology lies in the widespread adoption of molecular and genomic approaches, which can lead to improved patient outcomes and the identification of antibiotic-resistant strains. Continued advancements, education, and exploration of ethical implications are necessary to fully harness the potential of molecular and genomic techniques in medical microbiology.
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Affiliation(s)
- Poyasha A Goyal
- Microbiology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Nandkishor J Bankar
- Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Vaishnavi H Mishra
- Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Sonali K Borkar
- Community Medicine, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Jagadish G Makade
- Community Medicine, Datta Meghe Medical College, Datta Meghe Institute of Medical Sciences(DU), Wardha, IND
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Kang M, Kim S, Lee DB, Hong C, Hwang KB. Gene-specific machine learning for pathogenicity prediction of rare BRCA1 and BRCA2 missense variants. Sci Rep 2023; 13:10478. [PMID: 37380723 DOI: 10.1038/s41598-023-37698-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/26/2023] [Indexed: 06/30/2023] Open
Abstract
Machine learning-based pathogenicity prediction helps interpret rare missense variants of BRCA1 and BRCA2, which are associated with hereditary cancers. Recent studies have shown that classifiers trained using variants of a specific gene or a set of genes related to a particular disease perform better than those trained using all variants, due to their higher specificity, despite the smaller training dataset size. In this study, we further investigated the advantages of "gene-specific" machine learning compared to "disease-specific" machine learning. We used 1068 rare (gnomAD minor allele frequency (MAF) < 0.005) missense variants of 28 genes associated with hereditary cancers for our investigation. Popular machine learning classifiers were employed: regularized logistic regression, extreme gradient boosting, random forests, support vector machines, and deep neural networks. As features, we used MAFs from multiple populations, functional prediction and conservation scores, and positions of variants. The disease-specific training dataset included the gene-specific training dataset and was > 7 × larger. However, we observed that gene-specific training variants were sufficient to produce the optimal pathogenicity predictor if a suitable machine learning classifier was employed. Therefore, we recommend gene-specific over disease-specific machine learning as an efficient and effective method for predicting the pathogenicity of rare BRCA1 and BRCA2 missense variants.
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Affiliation(s)
- Moonjong Kang
- Research Center, Software Division, NGeneBio, Seoul, 08390, Korea
| | - Seonhwa Kim
- Research Center, Software Division, NGeneBio, Seoul, 08390, Korea
| | - Da-Bin Lee
- Department of Computer Science and Engineering, Graduate School, Soongsil University, Seoul, 06978, Korea
| | - Changbum Hong
- Research Center, Software Division, NGeneBio, Seoul, 08390, Korea.
| | - Kyu-Baek Hwang
- Department of Computer Science and Engineering, Graduate School, Soongsil University, Seoul, 06978, Korea.
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Kim ET, Jeong HE, Yoon HJ, Kim KH, Suh DS. Validation of multi-gene panel next-generation sequencing for the detection of BRCA mutation in formalin-fixed, paraffin-embedded epithelial ovarian cancer tissues. Taiwan J Obstet Gynecol 2023; 62:66-70. [PMID: 36720553 DOI: 10.1016/j.tjog.2022.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVE The therapeutic effect of poly (ADP-ribose) polymerase (PARP) inhibitors in patients with epithelial ovarian cancer (EOC) with somatic BRCA mutations is consistent with that observed in patients with germline BRCA mutations, indicating the importance of detecting both germline and somatic BRCA mutations concurrently. We compared the efficacy of multi-gene panel next generation sequencing (NGS) in EOC patients' formalin-fixed, paraffin-embedded (FFPE) tissue to that of conventional Sanger sequencing in blood samples. MATERIALS AND METHODS This study included 48 patients with EOC, and both blood Sanger sequencing and FFPE tissue NGS were conducted in all of them. Clinical and pathological data were reviewed, including age at diagnosis, histology, and stage. Blood Sanger sequencing was performed using peripheral blood leukocytes. The target regions of 90 cancer-related genes were identified using FFPE tissue. RESULTS The median age of patients was 56.1 years, with serous carcinoma (n = 40, 83.3%) and stage III (n = 37, 77.1%) being the most common histology and International Federation of Gynecology and Obstetrics (FIGO) stage, respectively. FFPE tissue NGS identified ten pathogenic variants, including all eight pathogenic variants identified by blood Sanger sequencing and two additional pathogenic variants. Furthermore, FFPE tissue NGS identified 19 variants of uncertain significance (VUS), including all ten VUS identified by blood Sanger sequencing and nine additional VUS. CONCLUSION The FFPE tissue multi-gene panel NGS had 100% sensitivity for detecting BRCA germline mutations and could detect additional somatic mutations. Furthermore, performing FFPE tissue multi-gene panel NGS followed by blood Sanger sequencing sequentially may help differentiate germline from somatic BRCA mutations for genetic counseling.
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Affiliation(s)
- Eun Taeg Kim
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Ha Eun Jeong
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Hyung Joon Yoon
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Ki Hyung Kim
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Dong Soo Suh
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea.
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8
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Gray SW, Ottesen RA, Currey M, Cristea M, Nikowitz J, Shehayeb S, Lozano V, Hom J, Kilburn J, Lopez LN, Wing S, Sosa E, Shen J, Morris M, Dilsizian B, Joseph T, Shen J, Adeimy C, Phillips T, Bahadini B, Niland JC. Leveraging an Informatics Approach to Identify an Unmet Clinical Need for BRCA1/ 2 Testing Among Patients With Ovarian Cancer. JCO Clin Cancer Inform 2022; 6:e2200034. [PMID: 36049148 PMCID: PMC9470148 DOI: 10.1200/cci.22.00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/31/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Although BRCA1/2 testing in ovarian cancer improves outcomes, it is vastly underutilized. Scalable approaches are urgently needed to improve genomically guided care. METHODS We developed a Natural Language Processing (NLP) pipeline to extract electronic medical record information to identify recipients of BRCA testing. We applied the NLP pipeline to assess testing status in 308 patients with ovarian cancer receiving care at a National Cancer Institute Comprehensive Cancer Center (main campus [MC] and five affiliated clinical network sites [CNS]) from 2017 to 2019. We compared characteristics between (1) patients who had/had not received testing and (2) testing utilization by site. RESULTS We found high uptake of BRCA testing (approximately 78%) from 2017 to 2019 with no significant differences between the MC and CNS. We observed an increase in testing over time (67%-85%), higher uptake of testing among younger patients (mean age tested = 61 years v untested = 65 years, P = .01), and higher testing among Hispanic (84%) compared with White, Non-Hispanic (78%), and Asian (75%) patients (P = .006). Documentation of referral for an internal genetics consultation for BRCA pathogenic variant carriers was higher at the MC compared with the CNS (94% v 31%). CONCLUSION We were able to successfully use a novel NLP pipeline to assess use of BRCA testing among patients with ovarian cancer. Despite relatively high levels of BRCA testing at our institution, 22% of patients had no documentation of genetic testing and documentation of referral to genetics among BRCA carriers in the CNS was low. Given success of the NLP pipeline, such an informatics-based approach holds promise as a scalable solution to identify gaps in genetic testing to ensure optimal treatment interventions in a timely manner.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Sam Wing
- Health Economics and Outcomes Research, Intuitive Surgical, Sunnyvale, CA
| | | | - Jenny Shen
- The State University of New York at Stony Brook, Stony Brook, NY
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9
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Di Giacomo D, Di Domenico M, Defourny SVP, Malatesta D, Di Teodoro G, Martino M, Viola A, D’Alterio N, Cammà C, Modesto P, Petrini A. Validation of AmpliSeq NGS Panel for BRCA1 and BRCA2 Variant Detection in Canine Formalin-Fixed Paraffin-Embedded Mammary Tumors. Life (Basel) 2022; 12:life12060851. [PMID: 35743882 PMCID: PMC9225004 DOI: 10.3390/life12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/01/2022] Open
Abstract
Mammary carcinomas are the most common neoplasms observed in women and in female dogs. Canine mammary tumors show epidemiological, clinical, genetic, and prognostic characteristics comparable to human breast cancers. The recent introduction of next generation sequencing (NGS) technologies has greatly improved research and diagnostics for humans, while these new tools still need to be implemented in animal models. In this study we developed and validated an AmpliSeq Panel assay for the identification of BRCA variants in twenty-two different dogs. The amplicon mean coverage was 5499× and uniformity was higher than 98% in all samples. The results of germline single nucleotide variants (SNVs) and insertions/deletions (INDELs) were fully concordant regardless of the types of samples considered (blood, fresh and FFPE tissues). Moreover, despite the high DNA degradation observed in older FFPE blocks (>5 years), the assay allowed full coverage of all amplicons for downstream analyses. We consider the NGS panel developed in this study as a useful tool for expanding information on BRCA genes in the veterinary field and for human health from a comparative oncology perspective.
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Affiliation(s)
- Daniela Di Giacomo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
- Correspondence:
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Sabrina Vanessa Patrizia Defourny
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Daniela Malatesta
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Michele Martino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Antonello Viola
- Veterinary Practitioner, Centro Veterinario Nova Julia, Via Galileo Galilei 177, 64021 Giulianova, Italy;
| | - Nicola D’Alterio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy
| | - Paola Modesto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy;
| | - Antonio Petrini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (S.V.P.D.); (D.M.); (G.D.T.); (M.M.); (N.D.); (C.C.); (A.P.)
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10
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Angrisani A, Di Fiore A, Di Trani CA, Fonte S, Petroni M, Lospinoso Severini L, Bordin F, Belloni L, Ferretti E, Canettieri G, Moretti M, De Smaele E. Specific Protein 1 and p53 Interplay Modulates the Expression of the KCTD-Containing Cullin3 Adaptor Suppressor of Hedgehog 2. Front Cell Dev Biol 2021; 9:638508. [PMID: 33898425 PMCID: PMC8060498 DOI: 10.3389/fcell.2021.638508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
The Hedgehog (Hh) signaling pathway plays a crucial role in normal embryonic development and adult tissue homeostasis. On the other end, dysregulated Hh signaling triggers a prolonged mitogenic response that may prompt abnormal cell proliferation, favoring tumorigenesis. Indeed, about 30% of medulloblastomas (MBs), the most common malignant childhood cerebellar tumors, exhibit improper activation of the Hh signaling. The oncosuppressor KCASH2 has been described as a suppressor of the Hh signaling pathway, and low KCASH2 expression was observed in Hh-dependent MB tumor. Therefore, the study of the modulation of KCASH2 expression may provide fundamental information for the development of new therapeutic approaches, aimed to restore physiological KCASH2 levels and Hh inhibition. To this end, we have analyzed the TATA-less KCASH2 proximal promoter and identified key transcriptional regulators of this gene: Sp1, a TF frequently overexpressed in tumors, and the tumor suppressor p53. Here, we show that in WT cells, Sp1 binds KCASH2 promoter on several putative binding sites, leading to increase in KCASH2 expression. On the other hand, p53 is involved in negative regulation of KCASH2. In this context, the balance between p53 and Sp1 expression, and the interplay between these two proteins determine whether Sp1 acts as an activator or a repressor of KCASH2 transcription. Indeed, in p53–/– MEF and p53 mutated tumor cells, we hypothesize that Sp1 drives promoter methylation through increased expression of the DNA methyltransferase 1 (DNMT1) and reduces KCASH2 transcription, which can be reversed by Sp1 inhibition or use of demethylating agents. We suggest therefore that downregulation of KCASH2 expression in tumors could be mediated by gain of Sp1 activity and epigenetic silencing events in cells where p53 functionality is lost. This work may open new venues for novel therapeutic multidrug approaches in the treatment of Hh-dependent tumors carrying p53 deficiency.
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Affiliation(s)
| | | | | | - Simone Fonte
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | | | | | - Fabio Bordin
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Laura Belloni
- Department of Internal, Anesthesiological and Cardiovascular Clinical Sciences, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University, Rome, Italy.,Istituto Pasteur, Fondazione Cenci-Bolognetti, Sapienza University, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University, Rome, Italy.,Istituto Pasteur, Fondazione Cenci-Bolognetti, Sapienza University, Rome, Italy
| | - Marta Moretti
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza University, Rome, Italy
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11
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Development and evaluation of a rapid and cost-efficient NGS-based MHC class I genotyping method for macaques by using a prevalent short-read sequencer. Immunogenetics 2021; 73:175-186. [PMID: 33447871 DOI: 10.1007/s00251-020-01199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 10/22/2022]
Abstract
Rhesus macaque is one of the most widely used primate model animals for immunological research of infectious diseases including human immunodeficiency virus (HIV) infection. It is well known that major histocompatibility complex (MHC) class I genotypes affect the susceptibility and disease progression to simian immunodeficiency virus (SIV) in rhesus macaques, which is resembling to HIV in humans. It is required to convincingly determine the MHC genotypes in the immunological investigations, that is why several next-generation sequencing (NGS)-based methods have been established. In general, NGS-based genotyping methods using short amplicons are not often applied to MHC because of increasing number of alleles and inevitable ambiguity in allele detection, although there is an advantage of short read sequencing systems that are commonly used today. In this study, we developed a new high-throughput NGS-based genotyping method for MHC class I alleles in rhesus macaques and cynomolgus macaques. By using our method, 95% and 100% of alleles identified by PCR cloning-based method were detected in rhesus macaques and cynomolgus macaques, respectively, which were highly correlated with their expression levels. It was noted that the simulation of new-allele detection step using artificial alleles differing by a few nucleotide sequences from a known allele could be identified with high accuracy and that we could detect a real novel allele from a rhesus macaque sample. These findings supported that our method could be adapted for primate animal models such as macaques to reduce the cost and labor of previous NGS-based MHC genotyping.
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12
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Jung SM, Ryu JM, Park HS, Park JS, Kang E, Lee S, Lee HB, Youn HJ, Yoo TK, Kim J, Lee JE, Han SA, Kim D, Kim SW. Trends in Risk-Reducing Mastectomy and Risk-Reducing Salpingo-Oophorectomy in Korean Carriers of the BRCA1/2 Mutation. J Breast Cancer 2020; 23:647-655. [PMID: 33408890 PMCID: PMC7779723 DOI: 10.4048/jbc.2020.23.e61] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Purpose BRCA1/2 mutations are associated with risks of breast and ovarian cancer. In Korea, incidences of BRCA1/2 genetic testing and risk-reducing surgery (RRS) have increased with insurance coverage and the Angelina Jolie effect. The aim of this study was to identify trends in RRS performed in Korean women with the BRCA1/2 mutation. Methods We retrospectively reviewed the medical records of BRCA1/2 mutation carriers with (affected carriers) and without (unaffected carriers) breast cancer until August 2018 from 25 Korean Hereditary Breast Cancer (KOHBRA)-affiliated hospitals. Results The numbers of contralateral risk-reducing mastectomy (RRM) and risk-reducing bilateral salpingo-oophorectomy (RRBSO) in affected carriers have increased 5.8- and 3.6-fold, respectively, since 2013. The numbers of RRBSO in unaffected carriers has increased 8-fold since 2013. The number of institutions that perform RRS has increased gradually. The number of hospitals that perform contralateral RRM on affected carriers increased from 3 in 2012 to 11 in 2018, and that of those that perform RRBSO increased from 7 to 17. The number of hospitals that perform bilateral RRM on unaffected carriers increased from 1 in 2012 to 2 in 2018, and that of those that perform RRBSO increased from 1 to 8. However, the hospitals showed differences in the rates of RRM or RRBSO performed. Conclusion The incidence of RRS increased each year throughout the study period. However, in Korea, the rate of RRS procedures depended on the hospital.
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Affiliation(s)
- Sung Mi Jung
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jai Min Ryu
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyung Seok Park
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Soo Park
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Eunyoung Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seeyoun Lee
- Department of Surgery, National Cancer Center, Goyang, Korea
| | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Jo Youn
- Division of Breast Thyroid Surgery, Department of Surgery, Jeonbuk National University Medical School, Jeonju, Korea
| | - Tae-Kyung Yoo
- Division of Breast Surgery, Department of Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jisun Kim
- Division of Breast Surgery, Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Jeong Eon Lee
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang Ah Han
- Department of Surgery, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Dongwon Kim
- Department of Surgery, Daerim St. Mary's Hospital, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Daerim St. Mary's Hospital, Seoul, Korea
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13
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Nicolussi A, Belardinilli F, Ottini L, Petroni M, Capalbo C, Giannini G, Coppa A. A novel BRCA2 splice variant identified in a young woman. Mol Genet Genomic Med 2020; 8:e1513. [PMID: 33159495 PMCID: PMC7767566 DOI: 10.1002/mgg3.1513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/07/2020] [Accepted: 09/02/2020] [Indexed: 11/08/2022] Open
Abstract
Background BRCA1/2 VUSs represent an important clinical issue in risk assessment for the breast/ovarian cancer families (HBOC) families. Among them, some occurring within the intron‐exon boundary may lead to aberrant splicing process by altering or creating de novo splicing regulatory elements or unmasking cryptic splice site. Defining the impact of these potential splice variants at functional level is important to establish their pathogenic role. Methods Genomic DNA was extracted from peripheral blood sample of a young woman affected with breast cancer belonging to a HBOC family and the entire coding regions of the BRCA1 and BRCA2 genes were amplified using the Ion AmpliSeq BRCA1 and BRCA2 Panel. The BRCA2 c.682‐2delA variant has been characterized by RT‐PCR analysis performed on mRNA extracted from blood and lymphoblastoid cell line. Results We demonstrated that a novel BRCA2 c.682‐2delA variant at the highly conserved splice consensus site in intron 8 disrupts the canonical splice acceptor site generating a truncated protein as predicted by several bioinformatics tools. Segregations analysis in the family and LOH performed on proband breast cancer tissue further confirmed its classification as pathogenic variant. Conclusion Combining different methodologies, we characterized this new BRCA2 variant and provided findings of clinical utility for its classification as pathogenic variant.
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Affiliation(s)
- Arianna Nicolussi
- Department of Experimental MedicineUniversity of Roma “La Sapienza”RomaItaly
| | | | - Laura Ottini
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
| | - Marialaura Petroni
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
| | - Carlo Capalbo
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
| | - Giuseppe Giannini
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
- Istituto Pasteur‐Fondazione Cenci BolognettiRomaItaly
| | - Anna Coppa
- Department of Experimental MedicineUniversity of Roma “La Sapienza”RomaItaly
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14
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Malhotra H, Kowtal P, Mehra N, Pramank R, Sarin R, Rajkumar T, Gupta S, Bapna A, Bhattacharyya GS, Gupta S, Maheshwari A, Mannan AU, Reddy Kundur R, Sekhon R, Singhal M, Smruti B, SP S, Suryavanshi M, Verma A. Genetic Counseling, Testing, and Management of HBOC in India: An Expert Consensus Document from Indian Society of Medical and Pediatric Oncology. JCO Glob Oncol 2020; 6:991-1008. [PMID: 32628584 PMCID: PMC7392772 DOI: 10.1200/jgo.19.00381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Hereditary breast and ovarian cancer (HBOC) syndrome is primarily characterized by mutations in the BRCA1/2 genes. There are several barriers to the implementation of genetic testing and counseling in India that may affect clinical decisions. These consensus recommendations were therefore convened as a collaborative effort to improve testing and management of HBOC in India. DESIGN Recommendations were developed by a multidisciplinary group of experts from the Indian Society of Medical and Pediatric Oncology and some invited experts on the basis of graded evidence from the literature and using a formal Delphi process to help reach consensus. PubMed and Google Scholar databases were searched to source relevant articles. RESULTS This consensus statement provides practical insight into identifying patients who should undergo genetic counseling and testing on the basis of assessments of family and ancestry and personal history of HBOC. It discusses the need and significance of genetic counselors and medical professionals who have the necessary expertise in genetic counseling and testing. Recommendations elucidate requirements of pretest counseling, including discussions on genetic variants of uncertain significance and risk reduction options. The group of experts recommended single-site mutation testing in families with a known mutation and next-generation sequencing coupled with multiplex ligation probe amplification for the detection of large genomic rearrangements for unknown mutations. Recommendations for surgical and lifestyle-related risk reduction approaches and management using poly (ADP-ribose) polymerase inhibitors are also detailed. CONCLUSION With rapid strides being made in the field of genetic testing/counseling in India, more oncologists are expected to include genetic testing/counseling as part of their clinical practice. These consensus recommendations are anticipated to help homogenize genetic testing and management of HBOC in India for improved patient care.
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Affiliation(s)
- Hemant Malhotra
- Department of Medical Oncology, Sri Ram Cancer Center, Mahatma Gandhi Medical College Hospital, Jaipur, India
| | - Pradnya Kowtal
- Sarin Laboratory and OIC Sanger Sequencing Facility, Advanced Centre for Treatment Research, and Education in Cancer, Navi Mumbai, India
| | - Nikita Mehra
- Department of Medical Oncology, Cancer Institute (WIA), Chennai, India
| | - Raja Pramank
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajiv Sarin
- Radiation Oncology, Cancer Genetics Unit, Tata Memorial Centre and PI Sarin Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | | | - Sudeep Gupta
- Tata Memorial Centre Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
| | - Ajay Bapna
- Department of Medical Oncology, Bhagwan Mahavir Cancer Hospital Research Center, Jaipur, India
| | | | - Sabhyata Gupta
- Department of Gynae Oncology, Medanta-The Medicity, Gurgaon, India
| | - Amita Maheshwari
- Department of Gynecologic Oncology, Tata Memorial Centre, Mumbai, India
| | - Ashraf U. Mannan
- Clinical Diagnostics, Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | | | - Rupinder Sekhon
- Gynae Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | | | - B.K. Smruti
- Bombay Hospital and Medical Research Centre, Mumbai, India
| | - Somashekhar SP
- Manipal Comprehensive Cancer Center, Manipal Hospital, Bengaluru, India
| | - Moushumi Suryavanshi
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Amit Verma
- Molecular Oncology and Cancer Genetics, Max Hospital, New Delhi, India
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15
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Belardinilli F, Capalbo C, Malapelle U, Pisapia P, Raimondo D, Milanetti E, Yasaman M, Liccardi C, Paci P, Sibilio P, Pepe F, Bonfiglio C, Mezi S, Magri V, Coppa A, Nicolussi A, Gradilone A, Petroni M, Di Giulio S, Fabretti F, Infante P, Coni S, Canettieri G, Troncone G, Giannini G. Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer. Front Oncol 2020; 10:560. [PMID: 32457828 PMCID: PMC7221020 DOI: 10.3389/fonc.2020.00560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Extensive molecular characterization of human colorectal cancer (CRC) via Next Generation Sequencing (NGS) indicated that genetic or epigenetic dysregulation of a relevant, but limited, number of molecular pathways typically occurs in this tumor. The molecular picture of the disease is significantly complicated by the frequent occurrence of individually rare genetic aberrations, which expand tumor heterogeneity. Inter- and intratumor molecular heterogeneity is very likely responsible for the remarkable individual variability in the response to conventional and target-driven first-line therapies, in metastatic CRC (mCRC) patients, whose median overall survival remains unsatisfactory. Implementation of an extensive molecular characterization of mCRC in the clinical routine does not yet appear feasible on a large scale, while multigene panel sequencing of most commonly mutated oncogene/oncosuppressor hotspots is more easily achievable. Here, we report that clinical multigene panel sequencing performed for anti-EGFR therapy predictive purposes in 639 formalin-fixed paraffin-embedded (FFPE) mCRC specimens revealed previously unknown pairwise mutation associations and a high proportion of cases carrying actionable gene mutations. Most importantly, a simple principal component analysis directed the delineation of a new molecular stratification of mCRC patients in eight groups characterized by non-random, specific mutational association patterns (MAPs), aggregating samples with similar biology. These data were validated on a The Cancer Genome Atlas (TCGA) CRC dataset. The proposed stratification may provide great opportunities to direct more informed therapeutic decisions in the majority of mCRC cases.
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Affiliation(s)
| | - Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Pasquale Pisapia
- Department of Public Health, University Federico II, Naples, Italy
| | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Mahdavian Yasaman
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Carlotta Liccardi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Paola Paci
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Pasquale Sibilio
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Francesco Pepe
- Department of Public Health, University Federico II, Naples, Italy
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Bari, Italy
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, Rome, Italy
| | - Valentina Magri
- Department of Surgery Pietro Valdoni, Faculty of Medicine and Dentistry, Sapienza University of Rome, Rome, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Sonia Coni
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| | | | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
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16
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Liptay M, Barbosa JS, Rottenberg S. Replication Fork Remodeling and Therapy Escape in DNA Damage Response-Deficient Cancers. Front Oncol 2020; 10:670. [PMID: 32432041 PMCID: PMC7214843 DOI: 10.3389/fonc.2020.00670] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/09/2020] [Indexed: 12/27/2022] Open
Abstract
Most cancers have lost a critical DNA damage response (DDR) pathway during tumor evolution. These alterations provide a useful explanation for the initial sensitivity of tumors to DNA-targeting chemotherapy. A striking example is dysfunctional homology-directed repair (HDR), e.g., due to inactivating mutations in BRCA1 and BRCA2 genes. Extensive efforts are being made to develop novel targeted therapies exploiting such an HDR defect. Inhibitors of poly(ADP-ribose) polymerase (PARP) are an instructive example of this approach. Despite the success of PARP inhibitors, the presence of primary or acquired therapy resistance remains a major challenge in clinical oncology. To move the field of precision medicine forward, we need to understand the precise mechanisms causing therapy resistance. Using preclinical models, various mechanisms underlying chemotherapy resistance have been identified. Restoration of HDR seems to be a prevalent mechanism but this does not explain resistance in all cases. Interestingly, some factors involved in DNA damage response (DDR) have independent functions in replication fork (RF) biology and their loss causes RF instability and therapy sensitivity. However, in BRCA-deficient tumors, loss of these factors leads to restored stability of RFs and acquired drug resistance. In this review we discuss the recent advances in the field of RF biology and its potential implications for chemotherapy response in DDR-defective cancers. Additionally, we review the role of DNA damage tolerance (DDT) pathways in maintenance of genome integrity and their alterations in cancer. Furthermore, we refer to novel tools that, combined with a better understanding of drug resistance mechanisms, may constitute a great advance in personalized diagnosis and therapeutic strategies for patients with HDR-deficient tumors.
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Affiliation(s)
- Martin Liptay
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Joana S. Barbosa
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
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17
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Zelli V, Compagnoni C, Cannita K, Capelli R, Capalbo C, Di Vito Nolfi M, Alesse E, Zazzeroni F, Tessitore A. Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. High Throughput 2020; 9:ht9010001. [PMID: 31936873 PMCID: PMC7151204 DOI: 10.3390/ht9010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Katia Cannita
- Medical Oncology Unit, St Salvatore Hospital, Via L. Natali 1, 67100 L’Aquila, Italy;
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Rome “La Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy;
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence:
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18
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Nicolussi A, Belardinilli F, Silvestri V, Mahdavian Y, Valentini V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Di Giulio S, Fabretti F, Fratini B, Gradilone A, Ottini L, Giannini G, Coppa A, Capalbo C. Identification of novel BRCA1 large genomic rearrangements by a computational algorithm of amplicon-based Next-Generation Sequencing data. PeerJ 2019; 7:e7972. [PMID: 31741787 PMCID: PMC6859874 DOI: 10.7717/peerj.7972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/30/2022] Open
Abstract
Background Genetic testing for BRCA1/2 germline mutations in hereditary breast/ovarian cancer patients requires screening for single nucleotide variants, small insertions/deletions and large genomic rearrangements (LGRs). These studies have long been run by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). The recent introduction of next-generation sequencing (NGS) platforms dramatically improved the speed and the efficiency of DNA testing for nucleotide variants, while the possibility to correctly detect LGRs by this mean is still debated. The purpose of this study was to establish whether and to which extent the development of an analytical algorithm could help us translating NGS sequencing via an Ion Torrent PGM platform into a tool suitable to identify LGRs in hereditary breast-ovarian cancer patients. Methods We first used NGS data of a group of three patients (training set), previously screened in our laboratory by conventional methods, to develop an algorithm for the calculation of the dosage quotient (DQ) to be compared with the Ion Reporter (IR) analysis. Then, we tested the optimized pipeline with a consecutive cohort of 85 uncharacterized probands (validation set) also subjected to MLPA analysis. Characterization of the breakpoints of three novel BRCA1 LGRs was obtained via long-range PCR and direct sequencing of the DNA products. Results In our cohort, the newly defined DQ-based algorithm detected 3/3 BRCA1 LGRs, demonstrating 100% sensitivity and 100% negative predictive value (NPV) (95% CI [87.6–99.9]) compared to 2/3 cases detected by IR (66.7% sensitivity and 98.2% NPV (95% CI [85.6–99.9])). Interestingly, DQ and IR shared 12 positive results, but exons deletion calls matched only in five cases, two of which confirmed by MLPA. The breakpoints of the 3 novel BRCA1 deletions, involving exons 16–17, 21–22 and 20, have been characterized. Conclusions Our study defined a DQ-based algorithm to identify BRCA1 LGRs using NGS data. Whether confirmed on larger data sets, this tool could guide the selection of samples to be subjected to MLPA analysis, leading to significant savings in time and money.
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Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Valentina Silvestri
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- U.O.C. Microbiology and Virology Laboratory, A.O. San Camillo Forlanini, Roma, Italy
| | - Marialaura Petroni
- Istituto Italiano di Tecnologia, Center for Life Nano Science @ Sapienza, Roma, Italy
| | - Massimo Zani
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sergio Ferraro
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Francesca Fabretti
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Beatrice Fratini
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Laura Ottini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
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